NAME

       chippeak  -  Locates  signal  peaks  within a set of tags positions produced by a ChIP-Seq
       experiment

SYNOPSIS

       chippeak [ options ] [ -f <feature name> ] -t <threshold> -w <window> -v <vicinity> [ <  ]
       [ SGA file ]

DESCRIPTION

       chippeak  reads  a  ChIP-seq data file (or from stdin [<]) in SGA format (<SGA file>), and
       detects signal peaks for ChIP-tag positions corresponding to a specific  feature  <feature
       name> when given.  If no feature is given then all input tags are processed.

       Launching  chippeak  without  any  arguments will print the options list, along with their
       default values.

       The <feature> parameter is a name that corresponds to the second field of  the  SGA  file.
       It  might  optionally include the strand specification (+|-).  If no feature is given then
       all input tags are processed.

       The SGA input file MUST BE sorted by sequence  name  (or  chromosome  id),  position,  and
       strand.  One should check the input SGA file with the following command:

       sort -s -c -k1,1 -k3,3n -k4,4 <SGA file>

       The output is an SGA-formatted list containing signal peak locations.

OPTIONS

       -c <cut-off>
              A value can be specified as a cut-off for the input tag counts.

              This parameter is optional. Its default value is 1.

       -d     Show  debug  info.  The  program performs the sorting order check of the input data
              file.

       -f <feature name>
              This parameter is used to select all or a sub-set  of  chIP-seq  input  tags.   The
              feature name is specified in the second field of the SGA-formatted input file.

              If no feature name is given, then all features are selected.

       -h     Show the usage message.

       -o     Oriented  strand  processing.  If  this  option  is  selected, peaks are separately
              detected on plus and minus strands, respectively.

       -r     Refine Peak Positions. If this option is selected, a post-processing step is turned
              on in order to improve peak location. For initially selected peaks, the position is
              recomputed as the center of gravity of the counts  in  the  regin  defined  by  the
              <window> parameter.

       -t <threshold>
              Peak  Threshold.  Cumulative  tag  count within a range w should be bigger or equal
              Threshold t.  The default value is 50.

              This parameter is optional.

       -v <vicinity>
              It defines the minimal distance (in bp) amongst a group of local maxima (high count
              values).

              This parameter is mandatory.

       -w <window>
              It defines the integration range (in bp) of signal (or tag) counts.

              This parameter is mandatory.

SEE ALSO

       chipcor(1) chipextract(1) chipcenter(1), chippart(1) chipscore(1),